Biotype and insecticide resistance status of Bemisia tabaci populations from Peninsular Malaysia

Bemisia tabaci, a resistance‐prone insect pest, is a cryptic species complex with important invasive biotypes such as B and Q. The biotype and resistance statuses of this pest in Malaysia remain unclear. This study assessed the biotype and resistance status of a number of contemporary populations of B. tabaci based on the mtCO1 marker and the dose‐response method, respectively. The Pahang (PHG) population was labelled as the Q biotype, while the remainder of the populations belonged to the Asia 1 biotype. A very low level of resistance for profenofos, cypermethrin, and imidacloprid was detected for all populations [resistance factor (RF) < 10]. Resistance to diafenthiuron ranged from very low to very high (RF > 100). All populations showed a very low level of resistance against pymetrozine except Q‐type PHG population, which exhibited a very high level of resistance. For most insecticides, the highest level of resistance was detected in the PHG population. The implications of these findings for better management of this noxious pest are discussed.     

Adaptive molecular evolution of MC1R gene reveals the evidence for positive diversifying selection in indigenous goat populations

Detecting signatures of selection can provide a new insight into the mechanism of contemporary breeding and artificial selection and further reveal the causal genes associated to the phenotypic variation. However, the signatures of selection on genes entailing for profitable traits between Chinese commercial and indigenous goats have been poorly interpreted. We noticed footprints of positive selection at MC 1R gene containing SNP s genotyped in five Chinese native goat breeds. An experimental distribution of F _ST was built based on approximations of F _ST for each SNP across five breeds. We identified selection using the high F _ST outlier method and found that MC 1R candidate gene show evidence of positive selection. Furthermore, adaptive selection pressure on specific codons was determined using different codon based on maximum‐likelihood methods; signature of positive selection in mammalian MC 1R was explored in individual codons. Evolutionary analyses were inferred under maximum likelihood models, the HyPhy package implemented in the DATAMONKEY Web Server. The results of codon selection displayed positive diversifying selection at the sites were mainly involved in development of genetic variations in coat color in various mammalian species. Positive diversifying selection inferred with recent evolutionary changes in domesticated goat MC 1R provides new insights that the gene evolution may have been modulated by domestication events in goats.     

Plasmid profiles of Neisseria gonorrhoeae in Peninsular Malaysia

The plasmid profiles of 160 strains of Neisseria gonorrhoeae isolated in Peninsular Malaysia, comprising 80 penicillinase-producing (PPNG) and 80 non-penicillinase-producing (non-PPNG) isolates, were determined. The 80 PPNG isolates were divided into two plasmid groups. All of them harbored two common plasmid species, a 4.4 megadalton (Md) R plasmid previously associated with beta-lactamase production in PPNG strains from the Far East and a 2.6 Md multicopy plasmid of unknown function. In addition to these two plasmids, 60 (75%) PPNG isolates also carried a large 24.5 Md conjugative plasmid. In contrast, the 80 non-PPNG strains were divided into three plasmid groups. All of them possessed the 2.6 Md cryptic plasmid, and 35 (44%) isolates also harbored the 24.5 Md transfer plasmid. Besides these two plasmids, one non-PPNG isolate carried an additional 7.8 Md cryptic plasmid.     

Mangrove sesarmid crab feeding experiments in Peninsular Malaysia

The feeding ecology of mangrove sesarmid crabs in Peninsular Malaysia was investigated by field and laboratory experiments using four mangrove leaf species (Avicennia officinalis, Bruguiera gymnorrhiza, B. parviflora and Rhizophora apiculata) and leaves of different condition (fresh and senescent). Leaves tethered on strings at high (Bruguiera zone) and low (Rhizophora zone) intertidal positions, both upstream (Sungai Pasir) and downstream (Lower Merbok) showed significant amounts of leaf litter removal in 24 h (mean 79±3% initial dry mass). Significantly more B. gymnorrhiza was consumed in Bruguiera zones and significantly less senescent A. officinalis in the upstream Rhizophora zone. In Bruguiera zones, significant numbers of leaves were taken down burrows but there were no preferences for leaf species or condition of leaf taken down burrows at all sites. In 24 h, under laboratory conditions, the sesarmid crabs Sesarma (Perisesarma) eumolpe and S. (Perisesarma) onychophorum were offered with a mangrove species choice of either fresh or senescent leaves. There was no difference in mangrove species taken when the leaves were senescent for both crab species, but when the leaves were fresh, significantly more A. officinalis leaves were consumed by both sesarmid crab species. S. onychophorum ate significantly more B. parviflora than did S. eumolpe. The crab distribution in the field was related to the preferred tree species dominance, indicating that tree species may be important for crab species distribution, or vice versa. The mean rate of leaf consumption was not significantly different between the crab species; S. eumolpe was 29.9±5.9 and S. onychophorum was 35.3±7.2 mg dry mass per wet mass gram of crab in 24 h. Rhizophora spp. were the least preferred species in all feeding experiments, a finding which may have implications for ecosystem functioning in monoculture rehabilitation projects.     

Ethnic fertility differentials in Peninsular Malaysia and Singapore

Differences in fertility between the three major ethnic groups (Malays, Chinese and Indians) in Peninsular Malaysia and Singapore have existed since before the onset of fertility decline in the late 1950s and remain today, although the relative positions and the actual differences have changed due to the varying rates of decline. By 1987, the Malays experienced the highest fertility and the Chinese the lowest in both countries but in Singapore the Malay fertility was lower than the Chinese fertility in Peninsular Malaysia. The fertility differentials will lead to changes in the ethnic composition in both countries but more so in Peninsular Malaysia.     

The ecology of mangrove forest birds in Peninsular Malaysia

The density, distribution and feeding ecology of birds of mangrove forests in Selangor on the west coast of Peninsular Malaysia were investigated between February and May 1989. Excluding aerial hunters and wading birds, 47 species were recorded from four mangrove forest sites in Selangor, though undoubtedly some rarer species were missed due to the brevity of the study. The estimated density of birds, using fixed-width transects, ranged from 15 to 26 birds per ha. One quarter of all birds counted belonged to just one species, the Ashy Tailorbird Orthotomus ruficeps. Excluding ground feeders (three species), four foraging guilds were recognized among 17 of the commonest bird species: obligate foliage-foraging insectivores (seven species), bark-foraging insectivores (four), facultative nectar-ivores (five) and aerial hawkers (one). Species within the first and third guilds apparently were partitioned by foraging technique and heights, while those of the second guild (woodpeckers) differed mainly in their selection of plant species. The horizontal distribution of several species corresponded to the zonation of mangroves. Avifaunal differences between sites reflected differences in forest floristics. The greatest number of species occurred at the dry landward edge site, which supported seven bird species not encountered elsewhere in Selangor. This habitat has almost completely disappeared from much of the peninsula owing to land reclamation. Four of the six resident mangrove-specialized bird species in Selangor were regularly recorded at two or more sites, another (Greater Gol-denback Woodpecker Chrysocolaptes lucidus) occurred at only one site and the last (Ruddy Kingfisher Halcyon coromanda) was never recorded. Two species of sunbirds probably play an important role in the pollination of several species of mangroves. The colonization of anthropogenic habitats by many mangrove-dwelling bird species is attributed partly to their generalized foraging niches, which may have evolved in response to regular fluctuations in food availability and the dynamic physiography of mangrove communities.     

Ecological aspects of endemic plant populations on Klang Gates quartz ridge,a habitat island in Peninsular Malaysia

The population characteristics of Aleisanthia rupestris (Rubiaceae), Eulalia milsumii (Poaceae) and Ilex praetermissa (Aquifoliaceae), endemic to the Klang Gates quartz ridge north-east of Kuala Lumpur, Malaysia were studied. Whereas their narrow, natural distribution within species-poor communities in drier, less fertile conditions on the ridge can be explained by the selection of adaptive traits and reduced plant competition compared to the more extensive, surrounding richer forest communities on more fertile soils, recent disturbances altering site conditions have diminished their populations. Populations were compared among various terrain and site conditions (ridge spine or rockface, exposed or sheltered) on less disturbed and very disturbed portions of the ridge. A. rupestris was scarce or absent in sites shaded by taller vegetation, probably an inability to establish in conditions associated with deeper soil development. I. praetermissa appeared specially adapted to rockfaces where unstable substrates and poor soil development may restrict competition with other plants. All three species were adversely affected to varying degrees by disturbance and altered site conditions; invasive, fast-spreading, thicket-forming, weeds in disturbed sites on gentler terrain on the ridge spine appear to be especially detrimental to A. rupestris and E. milsumii establishment. Although the larger plant size of I. praetermissa compared to the other two species could mean it is less likely to be shaded out by invading weedy species, residual adults as well as new regeneration may not adapt to changed site conditions following disturbance. Distinguishing between adaptation (of both adults and new regeneration) to changed environmental conditions following disturbance, and ability in competing for space and resources against invading weedy species, is relevant.     

Widespread positive selection in synonymous sites of mammalian genes

Evolution of protein sequences is largely governed by purifying selection, with a small fraction of proteins evolving under positive selection. The evolution at synonymous positions in protein-coding genes is not nearly as well understood, with the extent and types of selection remaining, largely, unclear. A statistical test to identify purifying and positive selection at synonymous sites in protein-coding genes was developed. The method compares the rate of evolution at synonymous sites (Ks) to that in intron sequences of the same gene after sampling the aligned intron sequences to mimic the statistical properties of coding sequences. We detected purifying selection at synonymous sites in approximately 28% of the 1,562 analyzed orthologous genes from mouse and rat, and positive selection in approximately 12% of the genes. Thus, the fraction of genes with readily detectable positive selection at synonymous sites is much greater than the fraction of genes with comparable positive selection at nonsynonymous sites, i.e., at the level of the protein sequence. Unlike other genes, the genes with positive selection at synonymous sites showed no correlation between Ks and the rate of evolution in nonsynonymous sites (Ka), indicating that evolution of synonymous sites under positive selection is decoupled from protein evolution. The genes with purifying selection at synonymous sites showed significant anticorrelation between Ks and expression level and breadth, indicating that highly expressed genes evolve slowly. The genes with positive selection at synonymous sites showed the opposite trend, i.e., highly expressed genes had, on average, higher Ks. For the genes with positive selection at synonymous sites, a significantly lower mRNA stability is predicted compared to the genes with negative selection. Thus, mRNA destabilization could be an important factor driving positive selection in nonsynonymous sites, probably, through regulation of expression at the level of mRNA degradation and, possibly, also translation rate. So, unexpectedly, we found that positive selection at synonymous sites of mammalian genes is substantially more common than positive selection at the level of protein sequences. Positive selection at synonymous sites might act through mRNA destabilization affecting mRNA levels and translation.     

Differential selection after duplication in mammalian developmental genes

Gene duplication provides the opportunity for subsequent refinement of distinct functions of the duplicated copies. Either through changes in coding sequence or changes in regulatory regions, duplicate copies appear to obtain new or tissue-specific functions. If this divergence were driven by natural selection, we would expect duplicated copies to have differentiated patterns of substitutions. We tested this hypothesis using genes that duplicated before the human/mouse split and whose orthologous relations were clear. The null hypothesis is that the number of amino acid changes between humans and mice was distributed similarly across different paralogs. We used a method modified from Tang and Lewontin to detect heterogeneity in the amino acid substitution pattern between those different paralogs. Our results show that many of the paralogous gene pairs appear to be under differential selection in the human/mouse comparison. The properties that led to diversification appear to have arisen before the split of the human and mouse lineages. Further study of the diverged genes revealed insights regarding the patterns of amino acid substitution that resulted in differences in function and/or expression of these genes. This approach has utility in the study of newly identified members of gene families in genomewide data mining and for contrasting the merits of alternative hypotheses for the evolutionary divergence of function of duplicated genes.     

Fusarium Species Associated with Mango Malformation in Peninsular Malaysia

Mango malformation has become the most important global disease on mango. Fusarium species previously associated with this disease include F. mangiferae, F. mexicanum, F. sterilihyphosum, F. proliferatum, F. subglutinans and F. tupiense. A few strains of F. proliferatum have been reported from Malaysia, but in this study, we report the results of more extensive sampling. The recovered strains were evaluated with morphology, mating tester strain cross‐fertility, amplified fragment length polymorphisms (AFLPs), and partial DNA sequences of the genes encoding translation elongation factor 1‐α (tef‐1α) and β‐tubulin (tub‐2). Amongst the 43 strains evaluated, three species were identified – F. proliferatum, F. mangiferae and F. subglutinans – with F. proliferatum being the most frequent (69%). None of the Fusarium species that appear to originate in the Americas were recovered in Malaysia, which suggests special measures may be warranted to keep these species from entering the country.     

Detection of Naegleria species in environmental samples from Peninsular Malaysia

Background

In Malaysia, researchers and medical practitioners are unfamiliar with Naegleria infections. Thus little is known about the existence of pathogenic Naegleria fowleri, and the resultant primary amoebic meningoencephalitis (PAM) is seldom included in the differential diagnosis of central nervous system infections. This study was conducted to detect the presence of Naegleria species in various environmental samples.

Methods/Findings

A total of 41 Naegleria-like isolates were isolated from water and dust samples. All these isolates were subjected to PCR using two primer sets designed from the ITS1-ITS2 regions. The N. fowleri species-specific primer set failed to produce the expected amplicon. The Naegleria genus-specific primers produced amplicons of 408 bp (35), 450 bp (2), 457 bp (2) or 381 bp (2) from all 41 isolates isolated from aquatic (33) and dust (8) samples. Analysis of the sequences from 10 representative isolates revealed that amplicons with fragments 408, 450 and 457 bp showed homology with non-pathogenic Naegleria species, and 381 bp showed homology with Vahlkampfia species. These results concurred with the morphological observation that all 39 isolates which exhibited flagella were Naegleria, while 2 isolates (AC7, {"type":"entrez-nucleotide","attrs":{"text":"JN034055","term_id":"347448982","term_text":"JN034055"}}JN034055 and AC8, {"type":"entrez-nucleotide","attrs":{"text":"JN034056","term_id":"347448983","term_text":"JN034056"}}JN034056) that did not exhibit flagella were Vahlkampfia species.

Conclusion

To date, pathogenic species of N. fowleri have not been isolated from Malaysia. All 39 isolates that produced amplicons (408, 450 and 457 bp) from the genus-specific primers were identified as being similar to nonpathogenic Naegleria. Amplicon 408 bp from 5 representative isolates showed 100% and 99.7% identity to Naegleria philippinensis isolate RJTM ({"type":"entrez-nucleotide","attrs":{"text":"AM167890","term_id":"83423362","term_text":"AM167890"}}AM167890) and is thus believed to be the most common species in our environment. Amplicons 450 bp and 457 bp were respectively believed to be from 2 new species of Naegleria, since representative isolates showed lower homology and had a longer base pair length when compared to the reference species in the Genbank, Naegleria schusteri ({"type":"entrez-nucleotide","attrs":{"text":"AJ566626","term_id":"37605481","term_text":"AJ566626"}}AJ566626) and Naegleria laresi ({"type":"entrez-nucleotide","attrs":{"text":"AJ566630","term_id":"37605485","term_text":"AJ566630"}}AJ566630), respectively.     

Microsatellite DNA markers indicate three genetic lineages in East Asian indigenous goat populations

The genetic differentiation and phylogenetic relationships of 18 indigenous goat populations from seven East Asian countries were analysed based on data obtained from 26 microsatellite DNA markers. The mean number of alleles (MNA) per population ranged from 2.5 to 7.6, with an average of 5.8. Genetic variability estimated from MNA and heterozygosity (H_E and H_O) were relatively low in coastal and island populations. A heterozygous deficiency within populations (F_IS = 0.054, P < 0.001) and total inbreeding (F_IT = 0.181, P < 0.01) were observed, and genetic differentiation in the populations (F_ST) was 13.4%. The results of Bayesian model‐based clustering and a neighbour‐joining tree based on Nei's genetic distance showed that Asian goat populations could be subdivided into at least the following three genetic clusters: East Asian, Southeast Asian and Mongolian. These results are in close accordance with conventional morphological and geographical classifications and migration history.     

Molecular identification of natural mangrove hybrids of Rhizophora in Peninsular Malaysia

Natural hybridization is common in plants. Very often, the identity of a putative hybrid is inferred based on the observation of morphological features intermediate between two possible parental species occurring in a specific location. However, due to plasticity of morphological features and the co-occurrence of more than two possible parental species, molecular markers would be most useful to establish the origin of a putative hybrid. In mangroves, three Rhizophora species (Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa) and two putative hybrids (Rhizophora × lamarckii and Rhizophora × annamalayana) are distributed in the Indo-West Pacific region. Leaf samples of Rhizophora were obtained from two locations in Peninsular Malaysia, namely, Bagan Lalang and Pulau Burung, where all three species grow in sympatry. We analyzed sequences of one chloroplast and six nuclear DNA regions. Our results confirmed earlier claims that the morphologically identified putative hybrids growing in Pulau Burung are R. × lamarckii, a cross between R. apiculata and R. stylosa. Our data also pointed to the possible discovery of a new Rhizophora hybrid—a cross between R. mucronata and R. stylosa—the identification of which would have been difficult based on morphological features alone. The directions and the stages of hybridization are also discussed.     

Identifying candidate positive selection genes in Korean imported pig breeds

Domestication and artificial selection have modified the genome landscape of the pig. The identification of selection signatures in the genome can help to elucidate the selection mechanisms and uncover the causal genes related to the phenotypic variations between domestic pig breeds. We scanned the genomes of Korean imported pig breeds against native breeds using Z-transformed Fst (ZF_ST) and Heterozygosity (ZH_p) statistics to search for the signatures of positive selection. We identified 411 (ZF_ST?=?175; ZH_p?=?256) putatively selected genes in commercial breeds. The gene regions identified were harboring those related to immunity, coat color, reproduction function and other traits. Several genes (e.g., PLSCR4, AGTR1 and CORIN) were related to reproduction traits such as fertility, ovulation rate, and uterine function. This study revealed genes which improve our understanding of the biological mechanisms of higher litter sizes, the phenotype of interest, in higher litter pig breeds.